In this tutorial, you will learn how to compare enrichment results in pathXcite, for example when comparing overlapping enriched concepts between two conditions or topics.
Step 1: Learn about Comparing Enrichment Results
Follow the steps below. Use ←/→ to navigate; press 1-9 to jump.
Step 1 of 5
The Comparison Module allows you to compare enrichment results between different conditions or topics.
Click on the "Compare Results" button in the main menu on the left.
Load two tsv files containing the enrichment results you want to compare. (These must be in the format as provided by the enrichment module.
Optional: you can set the gene set library which was used, too, such that the comparison lists this as well.
Click "Create Comparison" to create the interactive view
Click the Export button to export the interactive view.
Both enrichment results must be against the same gene set library, as the plot will be calculated based on shared ranked terms.
The Example Comparison View shows the results of the comparison between the two selected enrichment analyses. (To recreate this result follow these steps:)
Create a database for Ehlers-Danlos Syndrome and another database for Marfan syndrome.
Set the PubMed Central year filter until October 2025,
Retrieve the 100 most relevant PubMed Central articles for Ehlers-Danlos Syndrome (and later within the other database Marfan syndrome - independently).
Select the 50 genes with the highest GF-IDF scores, and perform enrichment analysis against the same gene set library (GO Biological Process 2025).
Export the results and create hence 2 separate enrichment result files.
Load both files in the Comparison Module.
Click "Create Comparison" and explore the results (which should look roughly like this:).
Nice! You can now dive into analysing the enrichment profiles' overlap.
